Gastrointestinal slow wave activity is, in part, responsible for governing gut motility. Dysrhythmic slow wave activity has been associated with a number of functional motility disorders, but the mechanisms involved are poorly understood. There exist a number of transgenic small animal models with functional motility disorders. However, current slow wave mapping methods are targeted towards humans and large animals and are not readily translatable. To overcome these shortcomings, a novel electrode array was developed using photolithography. The developed photolithographic electrode array (PEA) was experimentally validated in vivo against a standard flexible printed circuit (FPC) array for comparison. Mean amplitudes of 0.13 ± 0.06 mV and 0.88 ± 0.05 mV were reported by the PEA and the FPC array, respectively. Mean signal to noise ratios (SNR) of 13.4 ± 6.4 dB and 8.3 ± 5.1 dB were achieved for the PEA and the FPC array, respectively. Our findings showed that the PEA acquired slow wave signals with higher amplitude and SNR. In this study, we showed that microfabrication techniques could be successfully implemented with optimized resolution for the investigation of normal and abnormal slow wave activity in smaller animals, which will enable a better understanding of the pathophysiological mechanisms and aid in the diagnosis and treatment of gastrointestinal motility disorders.Clinical Relevance - The ability to characterize the slow wave activity in transgenic animals with functional motility disorders would be a critical advance for the diagnosis and treatment of these disorders. Microfabrication techniques enable miniaturization of high-resolution electrode arrays suitable for mapping electrical activity in normal and transgenic small laboratory animals such as rats and mice.